[R] Stepwise rQTL-unknown warning message and odd QTL curve
John Kane
jrkrideau at inbox.com
Sat May 23 19:40:36 CEST 2015
Hi Clare,
I suspect that we need to see some data in dput() format. See the links I sent earlier or have a look at ?dput for more information.
John Kane
Kingston ON Canada
> -----Original Message-----
> From: claire.oquin at uky.edu
> Sent: Sat, 23 May 2015 07:40:03 -0400
> To: ligges at statistik.tu-dortmund.de
> Subject: Re: [R] Stepwise rQTL-unknown warning message and odd QTL curve
>
> Sorry, I'll try to provide more detail about what I have done so far with
> code and any relevant output results.
>
> >library(qtl)
> >sawfly.cross <- read.cross(format="csv",
> file="~/Desktop/Sawfly_data/QTL/Sawfly_QTL.csv", na.strings="NA",
> genotypes=c("A", "B"), alleles=c("A", "B"), estimate.map=F)
> --Read the following data:
> 430 individuals
> 506 markers
> 19 phenotypes
> --Cross type: bc
>
> >print(sawfly.cross)
> --This is an object of class "cross".
> It is too complex to print, so we provide just this summary.
> Backcross
>
> No. individuals: 430
>
> No. phenotypes: 19
> Percent phenotyped: 99.8 99.8 99.3 99.1 99.1 99.1 99.1 99.1 99.5 99.8
> 99.8 99.5 98.8 99.8 99.8 99.8 99.8 98.4 99.5
>
> No. chromosomes: 7
> Autosomes: 1 2 3 4 5 6 7
>
> Total markers: 506
> No. markers: 103 89 75 74 65 51 49
> Percent genotyped: 96.2
> Genotypes (%): AA:49.7 AB:50.3
> Backcross
>
> No. individuals: 430
>
> No. phenotypes: 19
> Percent phenotyped: 99.8 99.8 99.3 99.1 99.1 99.1 99.1 99.1 99.5 99.8
> 99.8 99.5 98.8 99.8 99.8 99.8 99.8 98.4 99.5
>
> No. chromosomes: 7
> Autosomes: 1 2 3 4 5 6 7
>
> Total markers: 506
> No. markers: 103 89 75 74 65 51 49
> Percent genotyped: 96.2
> Genotypes (%): AA:49.7 AB:50.3
>
> >sawfly.cross <- calc.genoprob(sawfly.cross, step=2.5, error.prob=0.1,
> map.function="kosambi", stepwidth="fixed")
>
> **I am using head size as a covariant.**
>
> >head.covar <- pull.pheno(sawfly.cross, pheno.col=19)
> >sawfly.cross.stepwise.peryellow <- scantwo(sawfly.cross, pheno.col=2,
> model="normal", method="hk", addcovar=head.covar, use="all.obs",
> clean.output=F, verbose=T, n.perm=1000, batchsize=100);
> save.image("~/Desktop/Sawfly_data/QTL/SawflyQTL.RData")
> --Warning messages:
> 1: In checkcovar(cross, pheno.col, addcovar, intcovar, perm.strata, :
> Dropping 1 individuals with missing phenotypes.
>
> 2: In checkcovar(cross, pheno.col, addcovar, intcovar, perm.strata, :
> Dropping 1 individuals with missing covariates.
>
>> sawfly.cross.stepwise.peryellow.pen <- calc.penalties(alpha=0.05,
> perms=sawfly.cross.stepwise.peryellow)
>
>>> sawfly.cross.stepwise.peryellow.stepqtl <- stepwiseqtl(sawfly.cross,
> pheno.col=2, method="hk", max.qtl=10,
> penalties=sawfly.cross.stepwise.peryellow.pen , verbose=T,
> keeplodprofile=T, covar=head.covar, scan.pairs=F, keeptrace=T)
> --Error in covar[!hasmissing, , drop = FALSE] : incorrect number of
> dimensions
>
> **I corrected this with the next piece of code
>
> >sawfly.cross.stepwise.peryellow.stepqtl <- stepwiseqtl(sawfly.cross,
> pheno.col=2, method="hk", max.qtl=10,
> penalties=sawfly.cross.stepwise.peryellow.pen , verbose=T,
> keeplodprofile=T, covar=as.data.frame(sawfly.cross$pheno$Head.Area),
> scan.pairs=F, keeptrace=T)
>
> The stepwise than ran and I got to the point where I got the warning
> message I posted
>
> about:Warning message:
> In lastout[[i]] - (max(lastout[[i]]) - dropresult[rn == qn[i], 3]) :
> longer object length is not a multiple of shorter object length
>
> I proceeded to examine the output
>
> >sawfly.cross.stepwise.peryellow.stepqtl
> QTL object containing genotype probabilities.
>
> name chr pos n.gen
> Q1 1 at 106.1 1 106.11 2
> Q2 2 at 180.0 2 179.97 2
> Q3 3 at 181.9 3 181.91 2
> Q4 3 at 181.9 3 181.91 2
> Q5 5 at 142.5 5 142.50 2
>
> Formula: y ~ sawfly.cross$pheno$Head.Area + Q1 + Q2 + Q3 + Q4 + Q5 +
> Q4:Q5
>
> pLOD: 166.23
>
>
> In my late night of googling, I did see that the warning can indicate
> that
> dimensions of the arguments do not match, but I do not know how to
> translate that to my data or output.
>
> Thank you.
>
> On Sat, May 23, 2015 at 3:36 AM, Uwe Ligges
> <ligges at statistik.tu-dortmund.de
>> wrote:
>
>>
>>
>> On 23.05.2015 01:07, Claire O'Quin wrote:
>>> Hi There,
>>>
>>> I am running a stepwise QTL for a backcross and got the following
>>> warning
>>> message:
>>>
>>> Warning message:
>>> In lastout[[i]] - (max(lastout[[i]]) - dropresult[rn == qn[i], 3]) :
>>> longer object length is not a multiple of shorter object length
>>
>> So dimensions of the arguments may not match?
>>>
>>> I can not discern what this means. When I created my plot, the QTL
>>> curve
>> on
>>> chromosome 3 is very odd (tried attaching it), so I suspect that the
>>> warning is connected to that odd curve plot.
>>>
>>> I tried running the fitqtl just to see what would happen and got an
>>> error
>>> (Error in solve.default(t(Z) %*% Z, t(Z) %*% X) : system is
>> computationally
>>> singular: reciprocal condition number = 1.49755e-24).
>>>
>>> Any thoughts about what is going on?
>>
>> No, without knoing what the arguments and the actual code was.
>>
>> Best,
>> Uwe Ligges
>>
>>>
>>> Thank you,
>>> Claire
>>>
>>>
>>>
>>> -----------------------------------
>>> Claire O'Quin, PhD
>>> Postdoctoral Research Scholar
>>> University of Kentucky
>>> http://www.linnenlab.com/home.html
>>>
>>>
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>
>
>
> --
> -----------------------------------
> Claire O'Quin, PhD
> Postdoctoral Research Scholar
> University of Kentucky
> http://www.linnenlab.com/home.html
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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